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KatyBrown / CIAlign

MIT License
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keep_gaponly? #28

Closed ollenordesjo closed 3 years ago

ollenordesjo commented 3 years ago

Hello!

Quick q about the keep_gaponly option:

https://github.com/KatyBrown/CIAlign/blob/master/CIAlign/CIAlign.py#L115

Since it defaults to True, does it make sense to change the wording? remove_gaponly and default to False perhaps?

Thanks!

ollenordesjo commented 3 years ago

Ah, I may have been mistaken, just running with default will actually remove gaponly right? In that case, maybe some tweaking can be done to show that the default is False?

schnamo commented 3 years ago

Hi! Thank you for altering us to this problem, it is indeed misleading.

By default, gap-only columns will be removed, however, if "--keep_gaponly" is added to the CIAlign call, internally remove_gaponly will be set to false and therefore gaponly columns won't be removed. I hope this makes sense!

ollenordesjo commented 3 years ago

Thanks, makes perfect sense now having looked at it again, and thanks for the clarification!